In the last few years, biologists and computer scientists have claimed that the introduction of data science techniques in molecular biology has changed the characteristics and the aims of typical outputs (i.e. models) of such a discipline. In this paper we will critically examine this claim. First, we identify the received view on models and their aims in molecular biology. Models in molecular biology are mechanistic and explanatory. Next, we identify the scope and aims of data science (machine learning in (...) particular). These lie mainly in the creation of predictive models which performances increase as data set increases. Next, we will identify a tradeoff between predictive and explanatory performances by comparing the features of mechanistic and predictive models. Finally, we show how this a priori analysis of machine learning and mechanistic research applies to actual biological practice. This will be done by analyzing the publications of a consortium—The Cancer Genome Atlas—which stands at the forefront in integrating data science and molecular biology. The result will be that biologists have to deal with the tradeoff between explaining and predicting that we have identified, and hence the explanatory force of the ‘new’ biology is substantially diminished if compared to the ‘old’ biology. However, this aspect also emphasizes the existence of other research goals which make predictive force independent from explanation. (shrink)

In the last few years, biologists and computer scientists have claimed that the introduction of data science techniques in molecular biology has changed the characteristics and the aims of typical outputs (i.e. models) of such a discipline. In this paper we will critically examine this claim. First, we identify the received view on models and their aims in molecular biology. Models in molecular biology are mechanistic and explanatory. Next, we identify the scope and aims of data science (machine learning in (...) particular). These lie mainly in the creation of predictive models which performances increase as data set increases. Next, we will identify a tradeoff between predictive and explanatory performances by comparing the features of mechanistic and predictive models. Finally, we show how this a priori analysis of machine learning and mechanistic research applies to actual biological practice. This will be done by analyzing the publications of a consortium—The Cancer Genome Atlas—which stands at the forefront in integrating data science and molecular biology. The result will be that biologists have to deal with the tradeoff between explaining and predicting that we have identified, and hence the explanatory force of the ‘new’ biology is substantially diminished if compared to the ‘old’ biology. However, this aspect also emphasizes the existence of other research goals which make predictive force independent from explanation. (shrink)

Molecular biologists exploit information conveyed by mechanistic models for experimental purposes. In this article, I make sense of this aspect of biological practice by developing Keller’s idea of the distinction between ‘models of’ and ‘models for’. ‘Models of (phenomena)’ should be understood as models representing phenomena and are valuable if they explain phenomena. ‘Models for (manipulating phenomena)’ are new types of material manipulations and are important not because of their explanatory force, but because of the interventionist strategies they afford. This (...) is a distinction between aspects of the same model. In molecular biology, models may be treated either as ‘models of’ or as ‘models for’. By analysing the discovery and characterization of restriction–modification systems and their exploitation for DNA cloning and mapping, I identify the differences between treating a model as a ‘model of’ or as a ‘model for’. These lie in the cognitive disposition of the modeller towards the model: a modeller will look at a model as a ‘model of’ if interested in its explanatory force, or as a ‘model for’ if interested in the material manipulations it can possibly afford. (shrink)

This paper adds to the philosophical literature on mechanistic explanation by elaborating two related explanatory functions of idealisation in mechanistic models. The first function involves explaining the presence of structural/organizational features of mechanisms by reference to their role as difference-makers for performance requirements. The second involves tracking counterfactual dependency relations between features of mechanisms and features of mechanistic explanandum phenomena. To make these functions salient, we relate our discussion to an exemplar from systems biological research on the mechanism for countering (...) heat shock—the heat shock response system—in Escherichia coli bacteria. This research also reinforces a more general lesson: ontic constraint accounts in the literature on mechanistic explanation provide insufficiently informative normative appraisals of mechanistic models. We close by outlining an alternative view on the explanatory norms governing mechanistic representation. (shrink)

In this essay, I examine the role of dissimilarity in scientific representation. After briefly reviewing some of the philosophical literature which places a strong emphasis on the role of similarity, I turn to examine some work from Carroll and Borges which demonstrates that perfect similarity is not valuable in the representational use of maps. Expanding on this insight, I go on to argue that this shows that dissimilarity is an important part of the representational use of maps—a point I then (...) extend to the case of scientific representation. Relying on some work from Latour, I argue that dissimilarity plays an essential role in representational practice, by providing novel forms of manipulation and use which affords the achievement of various epistemic and nonepistemic aims. After showing how this point connects to some other literature on scientific representation, I discuss some examples of the value of dissimilarity in the use of representational vehicles. Overall, I argue that to understand scientific representation, we will need to consider more than just similarity. We will need to explore dissimilarities as well. (shrink)

Personalised medicine has been discussed as a medical paradigm shift that will improve health while reducing inefficiency and waste. At the same time, it raises new practical, regulatory, and ethical challenges. In this paper, we examine PM strategies epistemologically in order to develop capacities to address these challenges, focusing on a recently proposed strategy for developing patient-specific models from induced pluripotent stem cells so as to make individualised treatment predictions. We compare this strategy to two main PM strategies—stratified medicine and (...) computational models. Drawing on epistemological work in the philosophy of medicine, we explain why these two methods, while powerful, are neither truly personalised nor, epistemologically speaking, novel strategies. Both are forms of correlational black box. We then argue that the iPSC models would count as a new kind of black box. They would not rely entirely on mechanistic knowledge, and they would utilise correlational evidence in a different way from other strategies—a way that would enable personalised predictions. In arguing that the iPSC models would present a novel method of gaining evidence for clinical practice, we provide an epistemic analysis that can help to inform the practical, regulatory, and ethical challenges of developing an iPSC system. (shrink)

The ontic conception of explanation is predicated on the proposition that “explanation is a relation between real objects in the world” and hence, according to this approach, scientific explanation cannot take place absent such a premise. Despite the fact that critics have emphasized several drawbacks of the ontic conception, as for example its inability to address the so-called “abstract explanations”, the debate is not settled and the ontic view can claim to capture cases of explanation that are non-abstract, such as (...) causal relations between events. However, by eliminating the distinction between abstract and non-abstract explanations, it follows that ontic and epistemic proposals can no longer contend to capture different cases of explanation and either all are captured by the ontic view or all are captured by the epistemic view. On closer inspection, it turns out that the ontic view deals with events that fall outside the scientists’ scope of observation and that it does not accommodate common instances of explanation such as explanations from false propositions and hence it cannot establish itself as the dominant philosophical stance with respect to explanation. On the contrary, the epistemic conception does account for almost all episodes of explanation and can be described as a relation between representations, whereby the explanans transmit information to the explanandum and that this information can come, dependent on context, in the form of any of the available theories of explanation (law-like, unificatory, causal and non-causal). The range of application of the ontic view thus is severely restricted to trivial cases of explanation that come through direct observation of the events involved in an explanation and explanation is to be mostly conceived epistemically. (shrink)

Evidence-Based Medicine has little consideration for mechanisms and philosophers of science and medicine have recently made pleas to increase the place of mechanisms in the medical evidence hierarchy. However, in this debate the notions of mechanisms seem to be limited to 'mechanistic processes' and 'complex-systems mechanisms,' understood as 'componential causal systems'. I believe that this will not do full justice to how mechanisms are used in biological, psychological and social sciences and, consequently, in a more biopsychosocial approach to medicine. Here, (...) I propose, following (Kuorikoski, 2009), to pay more attention to 'abstract forms of interaction' mechanisms. The present work scrutinized review articles on depression and medically unexplained pain, which are considered to be of multifactorial pathogenesis, for their use of mechanisms. In review articles on these disorders there seemed to be a range of uses between more 'abstract forms of interaction' and 'componential causal system' mechanisms. I therefore propose to expand the notions of mechanisms considered in medicine to include that of more 'abstract forms of interaction' to better explain and manage biopsychosocial disorders. (shrink)

Abstraction and idealization are the two notions that are most often discussed in the context of assumptions employed in the process of model building. These notions are also routinely used in philosophical debates such as that on the mechanistic account of explanation. Indeed, an objection to the mechanistic account has recently been formulated precisely on these grounds: mechanists cannot account for the common practice of idealizing difference-making factors in models in molecular biology. In this paper I revisit the debate and (...) I argue that the objection does not stand up to scrutiny. This is because it is riddled with a number of conceptual inconsistencies. By attempting to resolve the tensions, I also draw several general lessons regarding the difficulties of applying abstraction and idealization in scientific practice. Finally, I argue that more care is needed only when speaking of abstraction and idealization in a context in which these concepts play an important role in an argument, such as that on mechanistic explanation. (shrink)

In this paper we assess the explanatory role of idealizations in ‘design explanations’, a type of functional explanation used in biology. In design explanations, idealizations highlight which factors make a difference to phenomena to be explained: hypothetical, idealized, organisms are invoked to make salient which traits of extant organisms make a difference to organismal fitness. This result negates the view that idealizations serve only pragmatic benefits, and complements the view that idealizations highlight factors that do not make a difference. This (...) analysis in particular strengthens the perspective that idealizations are means to highlight difference making factors, and identifies a novel, more direct role for idealizations in doing so. It thus offers a novel argument why in some explanatory contexts idealizations are in-eliminable. (shrink)

In this paper we assess the explanatory role of idealizations in ‘design explanations’, a type of functional explanation used in biology. In design explanations, idealizations highlight which factors make a difference to phenomena to be explained: hypothetical, idealized, organisms are invoked to make salient which traits of extant organisms make a difference to organismal fitness. This result negates the view that idealizations serve only pragmatic benefits, and complements the view that idealizations highlight factors that do not make a difference. This (...) analysis in particular strengthens the perspective that idealizations are means to highlight difference making factors, and identifies a novel, more direct role for idealizations in doing so. It thus offers a novel argument why in some explanatory contexts idealizations are in-eliminable. (shrink)

Scientific explanation is a perennial topic in philosophy of science, but the literature has fragmented into specialized discussions in different scientific disciplines. An increasing attention to scientific practice by philosophers is (in part) responsible for this fragmentation and has put pressure on criteria of adequacy for philosophical accounts of explanation, usually demanding some form of pluralism. This commentary examines the arguments offered by Fagan and Woody with respect to explanation and understanding in scientific practice. I begin by scrutinizing Fagan's concept (...) of collaborative explanation, highlighting its distinctive advantages and expressing concern about several of its assumptions. Then I analyze Woody's attempt to reorient discussions of scientific explanation around functional considerations, elaborating on the wider implications of this methodological recommendation. I conclude with reflections on synergies and tensions that emerge when the two papers are juxtaposed and how these draw attention to critical issues that confront ongoing philosophical analyses of scientific explanation. (shrink)

Research in pharmacogenomics and precision medicine has recently introduced the concept of Polygenic Scores (PGSs), namely, indexes that aggregate the effects that many genetic variants are predicted to have on individual disease risk. The popularity of PGSs is increasing rapidly, but surprisingly little attention has been paid to the idealisations they make about phenotypic development. Indeed, PGSs rely on quantitative genetics models and methods, which involve considerable theoretical assumptions that have been questioned on various grounds. This comes with epistemological and (...) ethical concerns about the use of PGSs in clinical decision-making. In this paper, I investigate to what extent idealisations in genetics models can impact the data gathering and clinical interpretation of genomics findings, particularly the calculation and predictive accuracy of PGSs. Although idealisations are considered ineliminable components of scientific models, they may be legitimate or not depending on the epistemic aims of a model. I thus analyse how various idealisations have been introduced in classical models and progressively readapted throughout the history of genetic theorising. Notably, this process involved important changes in the epistemic purpose of such idealisations, which raises the question of whether they are legitimate in the context of contemporary genomics. (shrink)

Species are considered the basic unit of biological classification and evolution. Hence, they are used as a benchmark in several fields, although the ontological status of such a category has always been a matter of debate. This paper aims to discuss the problem of the definition of species within the new mechanistic approach. Nevertheless, the boundary between entities, activities, and mechanisms remains difficult to establish and always requires an analysis of what is meant by explanation. As a case study, the (...) paper describes the debate concerning the species category by considering different kingdoms: Animals, Bacteria, and Fungi. The inherently biological differences between those groups prevent the use of a single, universally applicable concept of species that could fit the mechanisms responsible for the variability present in these kingdoms. The same issue is encountered within each group, as highlighted through a focus on mammals and microbes. This controversy has given rise to opposite approaches, namely: monism, which looks for a single definition that might account for all species, and pluralism, which admits that different groups of organisms require somewhat different definitions. In order to develop an adequate definition of species, we propose to apply a new mechanistic framework, which considers the ontic-epistemic dimensions of scientific explanation in close parallel. The apt correlation between epistemic and the ontic aspects highlights the way in which the concept of species and the reference to data are strictly co-determined. This suggests that the concept of species is better understandable within a dual ontic-epistemic approach. (shrink)

Reduction and reductionism have been central philosophical topics in analytic philosophy of science for more than six decades. Together they encompass a diversity of issues from metaphysics and epistemology. This article provides an introduction to the topic that illuminates how contemporary epistemological discussions took their shape historically and limns the contours of concrete cases of reduction in specific natural sciences. The unity of science and the impulse to accomplish compositional reduction in accord with a layer-cake vision of the sciences, the (...) seminal contributions of Ernest Nagel on theory reduction and how they strongly conditioned subsequent philosophical discussions, and the detailed issues pertaining to different accounts of reduction that arise in both physical and biological science (e.g., limit-case and part-whole reduction in physics, the difference-making principle in genetics, and mechanisms in molecular biology) are explored. The conclusion argues that the epistemological heterogeneity and patchwork organization of the natural sciences encourages a pluralist stance about reduction. (shrink)

Turing patterns are a class of minimal mathematical models that have been used to discover and conceptualize certain abstract features of early biological development. This paper examines a range of these minimal models in order to articulate and elaborate a philosophical analysis of their epistemic uses. It is argued that minimal mathematical models aid in structuring the epistemic practices of biology by providing precise descriptions of the quantitative relations between various features of the complex systems, generating novel predictions that can (...) be compared with experimental data, promoting theory exploration, and acting as constitutive parts of empirically adequate explanations of naturally occurring phenomena, such as biological pattern formation. Focusing on the roles that minimal model explanations play in science motivates the adoption of a broader diachronic view of scientific explanation. (shrink)